Heat of the moment, he didn't really notice anything. You barely even noticed it at the time yourself. It was afterwards when he actually realized.

Jonathan was grabbing you a glass of water, but just before he could actually hand it to you his hand pulled back. "Did you say Scarecrow, earlier?" He asked, despite being absolutely positive there was skepticism in his voice.

He pictured your hazy expression and how your voice hitched when it happened. He would brush it off and assume his memory was wrong but 'Jonathan' and 'Scarecrow' do not rhyme. At all. He found it funny if anything.